MADISON – Access to clean water is a fundamental part of public health, yet tests for the bacteria, viruses and protozoans that cause water-borne diseases are fundamentally little changed since Robert Koch helped pioneer the germ theory of disease in the 1880s.
Now, a fledgling company that emerged from the University of Wisconsin-Madison College of Engineering promises to change that by applying high-speed genetic sequencing to the difficult problem of detecting – and for the first time counting – these pathogens.
Today’s approaches are too slow and too specific, says Francisco Moya, CEO of Pathogenomica. “The problem with current techniques is that they require specific tests to identify each pathogen. You need to look one by one.”
Currently, organisms in samples are cultured in lab dishes, which can take up to two weeks. Then, after they have multiplied sufficiently, they are tested for pathogens. But each analysis aims at one specific pathogen.
There are many potential pathogens, but it’s expensive to test for them all – a task Moya likens to trying to open hundreds of locks. “With current technology, you would have to design a different key for each lock. It’s much simpler to come up with a master key. We call next-generation sequencing a master key because it can unlock all the known pathogens present in a sample.”
The battle for clean water is far from over, says Moya. The World Health Organization estimates that 842,000 people die each year due to problems with water supply, sanitation and hygiene.
Pathogenomica’s better idea focuses on telltale strands of genetic material that can be used to pinpoint the identity of bacteria, viruses and protozoans. One of these strands, called 16S rRNA, has been used for about 25 years to identify bacteria. But until recently, the necessary sequencing process has been too slow and expensive for routine use in a water quality lab.
No longer, says Moya, a Ph.D. candidate in civil and environmental engineering.
Once the company starts operating in a year or so, it will be a very simple process, he says. “The customer sends a sample, we do the sequencing, and we compare the results to a proprietary database to classify the microbes as pathogenic or non-pathogenic – a bad guy or a good guy.”
At that point, the customer receives a report, showing the identity of pathogens present, along with a risk assessment and an interactive diagram showing the classification of the microbes.
The entire process should take no longer than a week, Moya says.